Demonstrators converging on the G20 summit this evening began taking over squats on the border of London's Square Mile to use as bases from which to launch a series of co-ordinated "direct action" protests.

The occupation of four buildings prompted the first confrontations with police, and marked the start of two days in which officers are expected to play cat and mouse with protesters determined to bring the financial heart of the capital to a standstill.

Protests are expected to centre around the Bank of England, where anti-capitalists and anarchist groups will converge at noon, and the European Climate Exchange in Bishopsgate, where at 12.30pm environmental activists say they will "swoop" on to the street and set up an overnight camp.

Financial institutions across the capital are on high alert, with police fearing that dozens of small, organised cells of anarchists are planning to peel away from the main demonstrations to force their way into office buildings, tube stations or banks.

Protesters have circulated a map of City targets that includes the offices of scores of banks, law firms and energy companies. It identifies 138 targets across the City, with more than 50 financial institutions pinpointed, including some of those blamed for sparking the economic crisis.

Many offices in the City of London will be closed and boarded-up tomorrow, including branches the Royal Bank of Scotland and Lloyds TSB. Hundreds of workers have been told to work from home. Those who are venturing into work have been told to "dress down" to avoid potential attacks.

Organisers of the expressed dismay a their portrayal as violent thugs and accused police of exaggerating the threat. They did, however, say they feared police warnings of "very violent" clashes may have attracted agitators who will infiltrate the demonstrations.

Police earlier arrived at an occupied derelict pub, in Shoreditch, moments after supporters posted the address online, advertising it as "conversion space" "for all anti-G20 action … and almost ready for the summer of rage". Officers stopped and searched people entering the building. They arrested three, one on suspicion of assaulting a police officer, one for carrying a saw and one for going equipped with weapons.

Nearby, around a dozen protesters had barricaded themselves into an empty Victorian office block.

The activists, their faces covered with scarves, said they hoped to use it as a base for hundreds of other protesters arriving in the capital ahead of the summit.

Police sealed off the short street for a period with vans and around a dozen police officers.

"They were being quite heavy-handed for a while," said Charlotte, 24, a protester. "The police were opening people's wallets and pulling out cards to look at their name." Friends of hers had been arrested, she added.

Inside the cavernous office block around 40 protesters were planning how they could accommodate and feed others who might arrive.

At a meeting they planned rotas to search skips for food and arrange for friends to bring cooking equipment and other supplies.

On one wall of the meeting room an activist had written instructions in marker pen about what to do if you were arrested, including the telephone number of a firm of solicitors.

Five other activists affiliated to the group Climate Camp said they were stopped and searched under anti-terrorism legislation at a cafe around the corner from the squat.

"A lot of police came in and very forcefully told use they were stopping and searching under the Terrorism Act," said Bradley Day, 22.

"We were meeting in the cafe to organise food for our camp, so all they found on us were recipes for cakes and lists of ingredients." Scotland Yard said it had no record of the searches.

The majority of protesters are likely to attach themselves to one of three events. Climate Camp will alert around two thousands campaigners by text message about the whereabouts of their planned "camp", to be set up somewhere in the Square Mile. The provisional plan is to meet at 12:30pm at the Climate Exchange.

G20 Meltdown will see a coalitions of anti-capitalist, anarchist and single-issue protest groups converge on the Bank of England.

Four groups will walk to the Bank from separate tube stations. At 2pm, Stop the War Coalition is leading a separate march from the US Embassy in Grosvener Square to Trafalgar Square, to demand that Barack Obama pulls US troops out of Iraq and Afghanistan. Small bands of protesters have also indicated they may convene at the ExCeL Centre in Docklands, where the summit will take place tomorrow.

David Howarth MP, who yesterday mediated last-minute talks between protesters and police, warned there was still "mutual misunderstanding" between the sides. He said the meeting between Climate Camp organisers and Scotland Yard's Commander Bob Broadhurst and chief superintendent Ian Thomas, had been "business-like" and both sides had exchanged numbers.

But he was concerned police appeared to believe that causing disruption to commuters would warrant intervening to stop a demonstration.

"I still think the two sides have different views on what's proportional," he said. "Police still seemed to think that any disruption of traffic is worth stopping a demonstration for. It's a shame this meeting did not happen earlier – there are points of mutual misunderstanding and the police really don't like the way in which Climate Camp is a non-hierarchical organisation."

Police have still not met with the organisers of G20 Meltdown, although the co-ordinator of the group, Marina Pepper, has said she would "talk about the plans" with police.

Confrontations, she said, would only occur if police attempted to prevent the protesters from reaching their destination. "When you've got the side of right on your side you won't be stopped, will you?" she said, adding that protesters would be bringing pillows. "And yes, we are prepared to fight truncheon with pillow."